We report herein a method for the ultra-trace detection of TNT on p-aminothiophenol-functionalized silver nanoparticles coated on silver molybdate nanowires based on surface-enhanced Raman scattering (SERS). The method relies on π-donor–acceptor interactions between the π-acceptor TNT and the π-donor p,p′-dimercaptoazobenzene (DMAB), with the latter serving to cross-link the silver nanoparticles deposited on the silver molybdate nanowires. This system presents optimal imprint molecule contours, with the DMAB forming imprint molecule sites that constitute SERS “hot spots”. Anchoring of the TNT analyte at these sites leads to a pronounced intensification of its Raman emission. We demonstrate that TNT concentrations as low as 10−12 M can be accurately detected using the described SERS assay. Most impressively, acting as a new type of SERS substrate, the silver/silver molybdate nanowires complex can yield new silver nanoparticles during the detection process, which makes the Raman signals very stable. A detailed mechanism for the observed SERS intensity change is discussed. Our experiments show that TNT can be detected quickly and accurately with ultra-high sensitivity, selectivity, reusability, and stability. The results reported herein may not only lead to many applications in SERS techniques, but might also form the basis of a new concept for a molecular imprinting strategy.